| ucscSession-class {rtracklayer} | R Documentation |
An implementation of browserSession
for the UCSC genome browser.
Objects can be created by calls of the form
browserSession("ucsc", url =
"http://genome.ucsc.edu/cgi-bin").
url:"character" holding the
base URL of the UCSC browser. hguid:"numeric" holding the
user identification code.views:"environment" containing
a list stored under the name "instances". The list holds the instances of
browserView for this session.
Class "browserSession", directly.
browserView(object, segment =
genomeSegment(object), track = tracks(object), ...)browserView of segment with visible
tracks named in track. Arguments in ... correspond
to slots in the genomeSegment class and override those
in segment. browserViews(object)browserView instances for this session. genomeSegment(object)genomeSegment last displayed in this session. genomeSequence(object, segment, track = "Assembly")segment and track.
layTrack(object, track, name = names(track),
view = TRUE, format = "gff")name and formatted as
format.
trackSet(object, segment = genomeSegment(), name =
deparse(substitute(object)), format = "bed", table = NULL)trackSet with features in
segment from track named name. Some built-in tracks
have multiple series, each stored in a separate database
table. A specific table may be retrieved by passing its name in
the table parameter. The exported data is formatted
according to format.
tracks(object)ucscTrackModes(object)ucscTable(object)table
in segment from track as a data.frame. Michael Lawrence
browserSession for creating instances of this class.